No randomized clinical trial comparing treatment options for small saphenous vein (SSV) incompetence exists, and there is no clear evidence that this axis behaves the same as the great saphenous vein after treatment. This means that the existing literature base, centered on the treatment of great saphenous vein incompetence cannot simply be extrapolated to inform the management of SSV insufficiency. This trial compares the gold standard of conventional surgery and endovenous laser ablation (EVLA) in the management of SSV incompetence. Patients with unilateral, primary saphenopopliteal junction incompetence and SSV reflux were randomized equally into parallel groups receiving either surgery or EVLA. Patients were assessed at baseline and weeks 1, 6, 12, and 52. Outcomes included successful abolition of axial reflux on duplex, visual analog pain scores, recovery time, complication rates, Venous Clinical Severity Score, and quality of life profiling. A total of 106 patients were recruited and randomized to surgery (n = 53) or EVLA (n = 53). Abolition of SSV reflux was significantly higher after EVLA (96.2%) than surgery (71.7%) (P < 0.001). Postoperative pain was significantly lower after EVLA (P < 0.05), allowing an earlier return to work and normal function (P < 0.001). Minor sensory disturbance was significantly lower in the EVLA group (7.5%) than in surgery (26.4%) (P = 0.009). Both groups demonstrated similar improvements in Venous Clinical Severity Score and quality of life. EVLA produced the same clinical benefits as conventional surgery but was more effective in addressing the underlying pathophysiology and was associated with less periprocedural morbidity allowing a faster recovery. ( NCT00841178.).